Hi Justin
Thanks for the suggestions. However, I don't really want to stop the
molecule moving into the next image-I start off with an alkyl chain
where a large portion of the structure overlaps the pbc.
i.e C1-C2-C3 \\ C4-C5-C6
where || is the unit cell boundary. To see the whole alkyl chain I use
the graphics/representations/periodic tab in VMD. The problem is that
VMD will not allow me to draw a bond between C3 and C4 meaning I get
odd looking movies. VMD prefers to join the C3 to the C4 in the same
unit cell rather than the C4 sitting right next to it on the other
side of the pbc. This means long bonds stretching the length of my
unit cell and missing bonds between atoms sitting next to each other!
I have spent a while trying to solve this and have posted to the VMD
forum (as it is actually a problem with VMD and not gromacs).
If I could somehow do the same thing to the traj.xtc as I did to
confgro.out using genconf -nbox 2 2 2 that would solve my
visualisation problem. Do you know of a way to do this? Even a
round-about way? I suppose if I dumped each frame in the trajectory
as a pdb, used genbox on them to get a 2x2x2 box and then somehow
stuck them together into an .xtc this might work (but any suggestions
which are less messy are greatly appreciated!)
Jenny
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
Jennifer Williams wrote:
Hello,
I am trying to find a way around a visualisation problem I am
having in VMD. Some of my molecules go over periodic boundary
conditions meaning that bonds sometimes appear missing when looking
at movies (I am trying to fix this using wrap, unwrap and join in
VMD but as yet no luck).
I was wondering if there is a way in gromacs to multiply the number
of unit cells shown in a trajectory. i.e instead of a 1x1x1 I want
the new unit cell to be 2x2x2. This would mean the section of the
structure I want to zoom in doesn't go over the pbc.
For the confout.gro file I have done this using
genconf -nbox 2 2 2 -f confout.gro -o confbig.out
and this enables me to at least see a static image where all bonds
are present.
but in order to view a movie, I need to carry out something similar
on the traj.xtc file. I have seen that with trjconv there is the
option
-box Size for new cubic box
but my unit cell is not cubic, it is a parallelepiped. The cell
dimensions are :
4.64210 3.77847 1.89596 0.00000 0.00000 -2.18150 0.00000
0.00000 0.00000
I tried using this anyway with the following command:
trjconv -box 9.28414 8.72598 3.79192 -f traj.xtc -o trajbig.xtc
but the resulting .xtc file wouldn't load into VMD so I assume that
the .xtc file and the .gro file didn't match.
Correcting periodicity should alleviate some of the problems. Using
trjconv -pbc mol (or -pbc nojump) is typically the best first step.
-Justin
Any ideas?,
Thanks
Jenny
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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